Differential Gene Expression between Leaf and Rhizome in Atractylodes lancea: A Comparative Transcriptome Analysis
| Autor: | Hegang Liu, Liu Yanwen, Xiao Huang, Kun Yu, Qianqian Huang, Bi-Sheng Huang, Juan Deng |
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| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Genetics biology Illumina sequencing Rhizome formation Differentially expressed gene Plant Science lcsh:Plant culture tissue-specific genes biology.organism_classification Rhizome Transcriptome 03 medical and health sciences 030104 developmental biology rhizomatous plants Botany Gene expression Gene family lcsh:SB1-1110 Atractylodes lancea KEGG Functional genomics Gene transcription factor Original Research |
| Zdroj: | Frontiers in Plant Science, Vol 7 (2016) Frontiers in Plant Science |
| ISSN: | 1664-462X |
| DOI: | 10.3389/fpls.2016.00348 |
| Popis: | The rhizome of Atractylodes lancea is extensively used in the practice of Traditional Chinese Medicine because of its broad pharmacological activities. This study was designed to characterize the transcriptome profiling of the rhizome and leaf of Atractylodes lancea in an attempt to uncover the molecular mechanisms regulating rhizome formation and growth. Over 270 million clean reads were assembled into 92,366 unigenes, 58% of which are homologous with sequences in public protein databases (NR, Swiss-Prot, GO, and KEGG). Analysis of expression levels showed that genes involved in photosynthesis, stress response, and translation were the most abundant transcripts in the leaf, while transcripts involved in stress response, transcription regulation, translation, and metabolism were dominant in the rhizome. Tissue-specific gene analysis identified distinct gene families active in the leaf and rhizome. Differential gene expression analysis revealed a clear difference in gene expression pattern, identifying 1,518 up-regulated genes and 3,464 down-regulated genes in the rhizome compared with the leaf,, including a series of genes related to signal transduction, primary and secondary metabolism. Transcription factor (TF) analysis identified 42 TF families, with 67 and 60 TFs up-regulated in the rhizome and leaf, respectively. A total of 104 unigenes were identified as candidates for regulating rhizome formation and development. These data offer an overview of the gene expression pattern of the rhizome and leaf and provide essential information for future studies on the molecular mechanisms of controlling rhizome formation and growth. The extensive transcriptome data generated in this study will be a valuable resource for further functional genomics studies of A. lancea. |
| Databáze: | OpenAIRE |
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